AU2019310041B2 - Methods and systems for adjusting tumor mutational burden by tumor fraction and coverage - Google Patents

Methods and systems for adjusting tumor mutational burden by tumor fraction and coverage

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Publication number
AU2019310041B2
AU2019310041B2 AU2019310041A AU2019310041A AU2019310041B2 AU 2019310041 B2 AU2019310041 B2 AU 2019310041B2 AU 2019310041 A AU2019310041 A AU 2019310041A AU 2019310041 A AU2019310041 A AU 2019310041A AU 2019310041 B2 AU2019310041 B2 AU 2019310041B2
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fraction
expected
sample
tmb
mutational
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AU2019310041A1 (en
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Darya CHUDOVA
Helmy Eltoukhy
Stephen Fairclough
Elena HELMAN
Ariel JAIMOVICH
Justin I. ODEGAARD
Katie Julia QUINN
Eleen SHUM
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Guardant Health Inc
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    • G16B20/50Mutagenesis
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AU2019310041A 2018-07-23 2019-07-22 Methods and systems for adjusting tumor mutational burden by tumor fraction and coverage Active AU2019310041B2 (en)

Applications Claiming Priority (9)

Application Number Priority Date Filing Date Title
US201862702280P 2018-07-23 2018-07-23
US62/702,280 2018-07-23
US201862741770P 2018-10-05 2018-10-05
US62/741,770 2018-10-05
US201862782894P 2018-12-20 2018-12-20
US62/782,894 2018-12-20
US201962824246P 2019-03-26 2019-03-26
US62/824,246 2019-03-26
PCT/US2019/042882 WO2020023420A2 (en) 2018-07-23 2019-07-22 Methods and systems for adjusting tumor mutational burden by tumor fraction and coverage

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AU2019310041A1 AU2019310041A1 (en) 2021-02-04
AU2019310041B2 true AU2019310041B2 (en) 2025-11-20

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US (3) US11118234B2 (https=)
EP (1) EP3827100A2 (https=)
JP (2) JP7466519B2 (https=)
KR (1) KR20210038577A (https=)
CN (2) CN112752854B (https=)
AU (1) AU2019310041B2 (https=)
CA (1) CA3107983A1 (https=)
SG (1) SG11202100344WA (https=)
WO (1) WO2020023420A2 (https=)

Families Citing this family (61)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9424392B2 (en) 2005-11-26 2016-08-23 Natera, Inc. System and method for cleaning noisy genetic data from target individuals using genetic data from genetically related individuals
US11111543B2 (en) 2005-07-29 2021-09-07 Natera, Inc. System and method for cleaning noisy genetic data and determining chromosome copy number
US11939634B2 (en) 2010-05-18 2024-03-26 Natera, Inc. Methods for simultaneous amplification of target loci
US12152275B2 (en) 2010-05-18 2024-11-26 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US10316362B2 (en) 2010-05-18 2019-06-11 Natera, Inc. Methods for simultaneous amplification of target loci
US20190010543A1 (en) 2010-05-18 2019-01-10 Natera, Inc. Methods for simultaneous amplification of target loci
US11322224B2 (en) 2010-05-18 2022-05-03 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US9677118B2 (en) 2014-04-21 2017-06-13 Natera, Inc. Methods for simultaneous amplification of target loci
US12221653B2 (en) 2010-05-18 2025-02-11 Natera, Inc. Methods for simultaneous amplification of target loci
RU2671980C2 (ru) 2011-02-09 2018-11-08 Натера, Инк. Способы неинвазивного пренатального установления плоидности
US20140100126A1 (en) 2012-08-17 2014-04-10 Natera, Inc. Method for Non-Invasive Prenatal Testing Using Parental Mosaicism Data
US20180173846A1 (en) 2014-06-05 2018-06-21 Natera, Inc. Systems and Methods for Detection of Aneuploidy
US11479812B2 (en) 2015-05-11 2022-10-25 Natera, Inc. Methods and compositions for determining ploidy
RU2760913C2 (ru) 2016-04-15 2021-12-01 Натера, Инк. Способы выявления рака легкого
GB201618485D0 (en) 2016-11-02 2016-12-14 Ucl Business Plc Method of detecting tumour recurrence
CN111868260B (zh) 2017-08-07 2025-02-21 约翰斯霍普金斯大学 用于评估和治疗癌症的方法和材料
US12084720B2 (en) 2017-12-14 2024-09-10 Natera, Inc. Assessing graft suitability for transplantation
US12024738B2 (en) 2018-04-14 2024-07-02 Natera, Inc. Methods for cancer detection and monitoring
US12234509B2 (en) 2018-07-03 2025-02-25 Natera, Inc. Methods for detection of donor-derived cell-free DNA
WO2020023420A2 (en) 2018-07-23 2020-01-30 Guardant Health, Inc. Methods and systems for adjusting tumor mutational burden by tumor fraction and coverage
US20200258601A1 (en) * 2018-10-17 2020-08-13 Tempus Labs Targeted-panel tumor mutational burden calculation systems and methods
US11640859B2 (en) 2018-10-17 2023-05-02 Tempus Labs, Inc. Data based cancer research and treatment systems and methods
US10395772B1 (en) 2018-10-17 2019-08-27 Tempus Labs Mobile supplementation, extraction, and analysis of health records
EP3891755A4 (en) 2018-12-03 2022-09-07 Tempus Labs, Inc. IDENTIFICATION, EXTRACTION AND PREDICTION SYSTEM FOR CLINICAL CONCEPTS AND RELATED PROCEDURES
WO2020160414A1 (en) * 2019-01-31 2020-08-06 Guardant Health, Inc. Compositions and methods for isolating cell-free dna
US11705226B2 (en) 2019-09-19 2023-07-18 Tempus Labs, Inc. Data based cancer research and treatment systems and methods
CA3149504A1 (en) 2019-08-22 2021-02-25 Tempus Labs, Inc. Unsupervised learning and prediction of lines of therapy from high-dimensional longitudinal medications data
EP4110378A4 (en) * 2020-02-27 2024-03-13 Foundation Medicine, Inc. Mitigation of statistical bias in genetic sampling
GB202003669D0 (en) * 2020-03-13 2020-04-29 Univ Oxford Innovation Ltd Method for identifying neo-antigens
CA3173453A1 (en) * 2020-03-26 2021-09-30 Wai Yi Tsui Systems and methods for distinguishing pathological mutations from clonal hematopoietic mutations in plasma cell-free dna by fragment size analysis
CN111402952A (zh) * 2020-03-27 2020-07-10 深圳裕策生物科技有限公司 一种检测肿瘤异质性程度的方法及系统
US20210407623A1 (en) * 2020-03-31 2021-12-30 Guardant Health, Inc. Determining tumor fraction for a sample based on methyl binding domain calibration data
CN112116956B (zh) * 2020-09-29 2024-04-19 深圳裕策生物科技有限公司 一种基于二代测序的肿瘤单样本tmb检测方法及装置
JP2024513668A (ja) * 2021-03-05 2024-03-27 ガーダント ヘルス, インコーポレイテッド 分子応答を分析するための方法および関連する態様
WO2022262569A1 (zh) * 2021-06-18 2022-12-22 广州燃石医学检验所有限公司 一种用于区分体细胞突变和种系突变的方法
JP2024523401A (ja) * 2021-06-21 2024-06-28 ガーダント ヘルス, インコーポレイテッド コピー数情報に基づく組織起源分析のための方法および組成物
WO2022271159A1 (en) * 2021-06-22 2022-12-29 Foundation Medicine, Inc. Systems and methods for evaluating tumor fraction
EP4388091A2 (en) * 2021-08-20 2024-06-26 Guardant Health, Inc. Methods for simultaneous molecular and sample barcoding
US20250003008A1 (en) * 2021-11-05 2025-01-02 The Johns Hopkins University Methods for treatment of cancer
EP4430614A4 (en) * 2021-11-12 2025-12-17 Found Medicine Inc Circulating tumor DNA fraction and uses thereof
CN114155911A (zh) * 2021-12-08 2022-03-08 深圳基因家科技有限公司 一种矫正肿瘤突变负荷的方法及系统
WO2023133131A1 (en) * 2022-01-04 2023-07-13 Natera, Inc. Methods for cancer detection and monitoring
EP4466706A1 (en) * 2022-01-18 2024-11-27 NEC Laboratories Europe GmbH Methods of vaccine design
EP4567129A3 (en) 2022-02-02 2025-08-13 Guardant Health, Inc. Multifunctional primers for paired sequencing reads
CN114596918B (zh) * 2022-03-11 2023-03-24 苏州吉因加生物医学工程有限公司 一种检测突变的方法及装置
CN116200490B (zh) * 2022-07-25 2025-05-16 慧算基因科技(上海)有限公司 一种实体瘤微小病灶残留检测panel的筛选方法
CN115404275B (zh) * 2022-08-17 2023-07-11 中山大学·深圳 一种基于纳米孔测序技术评估肿瘤纯度的方法
WO2024112643A1 (en) * 2022-11-21 2024-05-30 Foundation Medicine, Inc. Fragmentomics based identification of tumor-specific copy number alteration states in liquid biopsy
EP4680766A1 (en) * 2023-03-13 2026-01-21 Grail, Inc. White blood cell contamination detection
WO2024215498A1 (en) * 2023-04-12 2024-10-17 Foundation Medicine, Inc. Method for detecting patients with systematically under-estimated tumor mutational burden who may benefit from immunotherapy
WO2024238750A2 (en) * 2023-05-17 2024-11-21 Foundation Medicine, Inc. Clonal hematopoiesis burden as a biomarker for immune checkpoint inhibitor response
WO2025049830A1 (en) * 2023-08-30 2025-03-06 Grail, Inc. Identification and exclusion of variants with outlier allele fractions in tumor fraction estimations
WO2025059338A1 (en) 2023-09-12 2025-03-20 Guardant Health, Inc. Methods for analyzing nucleic acids using sequence read family size distribution
WO2025064706A1 (en) 2023-09-19 2025-03-27 Guardant Health, Inc. Detecting the presence of a tumor based on methylation status of cell-free nucleic acid molecules
WO2025076452A1 (en) 2023-10-06 2025-04-10 Guardant Health, Inc. Detecting tumor-related information based on methylation status of cell-free nucleic acid molecules
WO2025096757A1 (en) 2023-11-01 2025-05-08 Sana Biotechnology, Inc. Hypoimmunogenic cd22-targeted car t cells for the treatment of relapsed and/or refractory b cell lymphomas
WO2025102060A1 (en) * 2023-11-10 2025-05-15 Caris Mpi, Inc. Accurate detection of origin of cell-free nucleic acids
WO2025122662A1 (en) * 2023-12-04 2025-06-12 Tempus Ai, Inc. Systems and methods for detecting somatic variants derived from circulating tumor nucleic acids
WO2025208044A1 (en) 2024-03-28 2025-10-02 Guardant Health, Inc. Methods for cancer detection using molecular patterns
US12467087B1 (en) 2024-06-25 2025-11-11 Guardant Health, Inc. Sequencing methods with partitioning
WO2026006432A2 (en) 2024-06-25 2026-01-02 Guardant Health, Inc. Sequencing methods with partitioning

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2017151524A1 (en) * 2016-02-29 2017-09-08 Foundation Medicine, Inc. Methods and systems for evaluating tumor mutational burden

Family Cites Families (57)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6582908B2 (en) 1990-12-06 2003-06-24 Affymetrix, Inc. Oligonucleotides
US20030017081A1 (en) 1994-02-10 2003-01-23 Affymetrix, Inc. Method and apparatus for imaging a sample on a device
DE69528706T2 (de) 1994-08-19 2003-06-12 Pe Corp. (Ny), Foster City Gekoppeltes ampflikation- und ligationverfahren
GB9620209D0 (en) 1996-09-27 1996-11-13 Cemu Bioteknik Ab Method of sequencing DNA
GB9626815D0 (en) 1996-12-23 1997-02-12 Cemu Bioteknik Ab Method of sequencing DNA
US6969488B2 (en) 1998-05-22 2005-11-29 Solexa, Inc. System and apparatus for sequential processing of analytes
AR021833A1 (es) 1998-09-30 2002-08-07 Applied Research Systems Metodos de amplificacion y secuenciacion de acido nucleico
US7501245B2 (en) 1999-06-28 2009-03-10 Helicos Biosciences Corp. Methods and apparatuses for analyzing polynucleotide sequences
US6818395B1 (en) 1999-06-28 2004-11-16 California Institute Of Technology Methods and apparatus for analyzing polynucleotide sequences
AU7537200A (en) 1999-09-29 2001-04-30 Solexa Ltd. Polynucleotide sequencing
US20020110538A1 (en) 1999-12-28 2002-08-15 Health Research, Inc. Methods and products for tumor immunotherapy using cytokines
US20030219765A1 (en) 2000-03-23 2003-11-27 Jose Costa Methods for evaluating cancer risk
ATE377093T1 (de) 2000-07-07 2007-11-15 Visigen Biotechnologies Inc Sequenzbestimmung in echtzeit
WO2003046146A2 (en) 2001-11-28 2003-06-05 Applera Corporation Compositions and methods of selective nucleic acid isolation
US7169560B2 (en) 2003-11-12 2007-01-30 Helicos Biosciences Corporation Short cycle methods for sequencing polynucleotides
WO2005108621A1 (en) 2004-04-30 2005-11-17 Yale University Methods and compositions for cancer diagnosis
CA2579150C (en) 2004-09-17 2014-11-25 Pacific Biosciences Of California, Inc. Apparatus and method for analysis of molecules
US7170050B2 (en) 2004-09-17 2007-01-30 Pacific Biosciences Of California, Inc. Apparatus and methods for optical analysis of molecules
US7482120B2 (en) 2005-01-28 2009-01-27 Helicos Biosciences Corporation Methods and compositions for improving fidelity in a nucleic acid synthesis reaction
US7282337B1 (en) 2006-04-14 2007-10-16 Helicos Biosciences Corporation Methods for increasing accuracy of nucleic acid sequencing
US8835358B2 (en) 2009-12-15 2014-09-16 Cellular Research, Inc. Digital counting of individual molecules by stochastic attachment of diverse labels
KR102759126B1 (ko) 2010-12-30 2025-01-24 파운데이션 메디신 인코포레이티드 종양 샘플의 다유전자 분석의 최적화
US11261494B2 (en) * 2012-06-21 2022-03-01 The Chinese University Of Hong Kong Method of measuring a fractional concentration of tumor DNA
US20160040229A1 (en) 2013-08-16 2016-02-11 Guardant Health, Inc. Systems and methods to detect rare mutations and copy number variation
CN104781421B (zh) 2012-09-04 2020-06-05 夸登特健康公司 检测稀有突变和拷贝数变异的系统和方法
US10876152B2 (en) 2012-09-04 2020-12-29 Guardant Health, Inc. Systems and methods to detect rare mutations and copy number variation
US9805407B2 (en) 2013-01-25 2017-10-31 Illumina, Inc. Methods and systems for using a cloud computing environment to configure and sell a biological sample preparation cartridge and share related data
WO2014151117A1 (en) 2013-03-15 2014-09-25 The Board Of Trustees Of The Leland Stanford Junior University Identification and use of circulating nucleic acid tumor markers
US10930368B2 (en) 2013-04-03 2021-02-23 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
ES3022582T3 (en) 2013-05-10 2025-05-28 Found Medicine Inc Analysis of genetic variants
ES2764096T3 (es) 2013-08-19 2020-06-02 Abbott Molecular Inc Bibliotecas de secuenciación de próxima generación
EP3090066A4 (en) 2014-01-02 2017-08-30 Memorial Sloan Kettering Cancer Center Determinants of cancer response to immunotherapy
US20150292033A1 (en) 2014-04-10 2015-10-15 Dana-Farber Cancer Institute, Inc. Method of determining cancer prognosis
CN107075730A (zh) * 2014-09-12 2017-08-18 利兰·斯坦福青年大学托管委员会 循环核酸的鉴定及用途
KR20230030022A (ko) 2014-11-13 2023-03-03 더 존스 홉킨스 유니버시티 관문 차단 및 미소부수체 불안정성
MA40737A (fr) 2014-11-21 2017-07-04 Memorial Sloan Kettering Cancer Center Déterminants de la réponse d'un cancer à une immunothérapie par blocage de pd-1
EP3766986B1 (en) * 2014-12-31 2022-06-01 Guardant Health, Inc. Detection and treatment of disease exhibiting disease cell heterogeneity and systems and methods for communicating test results
HUE058263T2 (hu) 2015-02-10 2022-07-28 Univ Hong Kong Chinese Mutációk detektálása rákszûrési és magzatelemzési célból
WO2016145578A1 (en) 2015-03-13 2016-09-22 Syz Cell Therapy Co. Methods of cancer treatment using activated t cells
WO2017073774A1 (ja) * 2015-10-28 2017-05-04 大日本印刷株式会社 電池用包装材料、電池、電池用包装材料の製造方法、及びアルミニウム合金箔
US10364468B2 (en) 2016-01-13 2019-07-30 Seven Bridges Genomics Inc. Systems and methods for analyzing circulating tumor DNA
JP6821693B2 (ja) 2016-02-29 2021-01-27 ジェネンテック, インコーポレイテッド がんのための治療方法及び診断方法
CA3015913A1 (en) 2016-02-29 2017-09-08 Foundation Medicine, Inc. Methods of treating cancer
TWI910495B (zh) 2016-05-13 2026-01-01 美商再生元醫藥公司 藉由投予pd-1抑制劑治療皮膚癌之方法
US10711312B2 (en) * 2016-07-12 2020-07-14 The Regents Of The University Of California Methods for immunotherapy-based treatment and assessment of cancer
US10294518B2 (en) 2016-09-16 2019-05-21 Fluxion Biosciences, Inc. Methods and systems for ultra-sensitive detection of genomic alterations
CA3038712A1 (en) 2016-10-06 2018-04-12 Genentech, Inc. Therapeutic and diagnostic methods for cancer
MX2019007444A (es) 2016-12-22 2019-08-16 Guardant Health Inc Metodos y sistemas para analisis de moleculas de acido nucleico.
US20180282417A1 (en) 2017-03-31 2018-10-04 Medimmune, Llc Tumor burden as measured by cell free dna
JP7760242B2 (ja) 2017-07-21 2025-10-27 ジェネンテック, インコーポレイテッド がんの治療法及び診断法
CA3075932A1 (en) 2017-09-20 2019-03-28 Guardant Health, Inc. Methods and systems for differentiating somatic and germline variants
WO2019090156A1 (en) 2017-11-03 2019-05-09 Guardant Health, Inc. Normalizing tumor mutation burden
WO2019108807A1 (en) 2017-12-01 2019-06-06 Personal Genome Diagnositics Inc. Process for microsatellite instability detection
US20210054465A1 (en) 2018-05-03 2021-02-25 Roche Sequencing Solutions, Inc. Surrogate marker and method for tumor mutation burden measurement
WO2019236478A1 (en) 2018-06-04 2019-12-12 Guardant Health, Inc. Methods and systems for determining the cellular origin of cell-free nucleic acids
WO2020023420A2 (en) 2018-07-23 2020-01-30 Guardant Health, Inc. Methods and systems for adjusting tumor mutational burden by tumor fraction and coverage
US20200258601A1 (en) 2018-10-17 2020-08-13 Tempus Labs Targeted-panel tumor mutational burden calculation systems and methods

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2017151524A1 (en) * 2016-02-29 2017-09-08 Foundation Medicine, Inc. Methods and systems for evaluating tumor mutational burden

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